[PyMOL] smoothed path through protein?

[Seth H. <sh...@ms...>]

Hi all,

I was wondering if one has access to the coordinates of the old 
smoothed ribbon path through the protein or some good ideas on how to 
calculate such a path.  I wanted to have the ribbon_rider script I 
wrote earlier follow such a path to avoid the jarring switching of 
directions it currently does at each alpha carbon waypoint.  I hoped 
that breaking up the path into small enough bits (i.e. doing the 
mvSinviewtravel thing one frame at a time and recalculating the 
direction at each step) would achieve this.  Perhaps it's mostly a 
question for Warren, then, if he can tell me how the old ribbon path 
was calculated.
A second refinement of this approach would be to have the path travel 
down the center of alpha helices rather than curling around to each 
Calpha but I wasn't sure if a running average approach would 
guarantee this behavior as I could imagine the trajectory hugging 
along one edge of a helix.

upgraded script version available shortly as I now have it working 
from the command line rather than just from scripts.

Thanks for any ideas,
seth
-- 
Seth Harris, Ph.D.
Agard Laboratory Suite S416
Box 2240
UCSF/HHMI
600 16th Street
San Francisco, CA 94143-2240
(Shipping Zip 94158)
415.502.2930